Consumed By Sin
by haze1982
Summary: After "Journey's End", the Doctor feels lost about everything that's happened recently. The loss of his companions and the last words of Davros are eating him from the inside out. While on holiday in San Francisco, he meets up with an unruly FBI Agent and an Assistant Director who wants to help. Future M/M Corporal Punishment (spanking) will be in this story.
1. Chapter 1

Consumed By Sin

Chapter One

The Doctor and the Agent

 _"The Meeting"_

 _ **Summary**_ _: After "Journey's End", the Doctor feels lost about everything that's happened recently. The loss of his companions and the last words of Davros are eating him from the inside out. The titles that he has earned are starting to get the better of him, so he decides to take a trip back when things were more simple. While on holiday in San Francisco, he meets up with an unruly FBI Agent known as Fox Mulder of the X-Files and an Assistant Director who's tired of Mulder's senseless actions._

* * *

 **San Francisco, California**

 **1997 Springtime**

 **8:30 p.m.**

The FBI Agent sat back in his rented Buick Century and watched the sun set beyond the horizon. He continued to nibble on his sunflower seeds, tossing out the shells, and sipped on his drink. The spring air was relaxing and the weather had been gorgeous the last few days. Fox Mulder decided to embark on another self-assigned mission. He thumbed though his files that he'd brought with him.

Part of him actually thought of calling the entire investigation off. That was the logical part that he told to shut up, thank you very much.

Of course, Scully thought that the entire notion of him giving a second thought to a Blue Box Alien was absurd, but for some reason or another he could not shake the sightings that he had read.

He read through the files as he chewed on his seeds. First sighting was in the early 1960s when a strange young girl went missing along with two schoolteachers in Britain. They reportedly were interested in her advanced knowledge of science well beyond her years. At this moment, he felt that any lead on disappearances may be able to lead him into the discovery of what happened to his sister.

Any lead in contacting Samantha were worth any trouble he would potentially get into with the FBI or Skinner.

As he continued to read the file on the Doctor, which was mostly comprised of data he could get his hands on - courtesy of the Lone Gunmen. Fox's cellular phone rang. He rolled his eyes as he noticed it was Skinner on the line and shook his head.

"To answer or not to answer...that is the question."

He took a quick drink of his sweet tea and took in a deep breath for strength. He hovered his thumb over the 'answer' button and accepted the phone call.

"Mulder."

"Agent Mulder. Where are you? And it better be within distance of the Bureau for the sake of your own ass."

"Well, I believe there may be one close to San Francisco."

"What are you doing in San Francisco?"

"On a lead from an old case. The paperwork is approved, Sir. I'll be back by the end of the week."

Skinner rubbed the bridge of his nose and clenched his jaw. "Fox, this trip was not approved by me. Our arrangement is that you are to let me know your whereabouts and, up until now, you've been ignoring my calls."

"Well…"

"Well, what? And the truth, Mulder."

"I knew you wouldn't allow this trip to be honest. I do have a good lead on alien sightings. I just need a few more days-"

"You will get on a plane and back to D.C. And I don't mean tomorrow or the next day. You will-"

"I'm sorry? What was that?"

"Fox!"

"We have a bad connection. I. Can't. Hear. You…." Mulder smirked to himself and hung up the phone. Putting the car in gear, he looked at his watch and decided to head back to the hotel. It was a long shot to even expect the Police box would show up but he had to try.

He took off his jacket and threw it in the backseat.

"Guess I'll call it a night."

He drove off in his rented vehicle and back to the hotel. The last time The Doctor showed up on this side of the pond was in this general vicinity, hopefully, he'll show soon.

 **####**

 **London, UK**

 **2008**

 **11:47 p.m.**

 _Never forget. I forever name you the destroyer of worlds. Ice, fire, and rage. The last of the Time Lords._

The words kept ringing in the tenth incarnation of the Doctor's head. All these titles he'd earned for himself and he couldn't disagree with any of them. He had destroyed his home, Gallifrey, and all that went along with it.

The only other Time Lord had since refused to regenerate, leaving him alone. The memories of the great Time War still dwell in his mind, as well as those memories of his past regenerations. Everything he had done up until now has led him to this moment.

A wonderful, fiery companion who was every bit as clever as he could hope for could no longer even remember who he was. He had to take away the memories from her or else she'd be another casualty. The raindrops trickled down his face as he leaned over the console of his faithful Tardis.

The two heartbeats deep inside his chest were aching. The hearts that have felt more hurt in the last century than he would have liked to. He would like to go back to his own home of Gallifrey but that wasn't even a choice.

He remembered the time before all this. Before the war. Before having to say goodbye to everything he loved.

He was in San Francisco and had been shot by a gang. The human doctor that tried to help him only wound up killing him due to the lack of knowledge to his physiology.

A time that everything was still right in the world for the most part.

He had lost so much: Rose, the death of the Master, Jack couldn't go along with him, Martha, and now Donna. He took in a deep breath and rubbed his face frantically. He didn't want to risk going at the precise time as his seventh incarnation of himself and he may accidentally meet, so he decided to go for a few years before the shooting happened.

"Right, old girl. Buena Vista Park. San Francisco. 1997. Let's take a bit of a holiday, alright?" He said to his Tardis and rubbed his hand gently over the console. "Just you and me."

He tapped the console and set the time.

"Let's go for 1997, then. Springtime. It has to be fantastic weather right now."

With that, he held on to the Tardis as it made its way through the vortex.

All that could be heard, if there was anyone around to hear it, was "Alllllllllons-y!"

 **####**

 **San Francisco**

 **1997**

 **10:15 p.m.**

"Hello, Mr. Brenner. I'm here to pay for the rest of the week. How much do I owe you?"

"Yes, yes. Mr. Mulder is it? That'll be $208.74. How are you enjoying San Francisco?"

"Fine, fine. Thanks. Buena Vista Park is rather nice."

"Hmm. It is if you like that sort of thing. Be careful of who you'll meet there."

"I'll be fine."

"Are you enjoying your room? Sorry we didn't have any lower floor rooms."

"The second floor will be perfectly fine. Sleep good, Sir."

"You, too."

Mulder climbed up the stairs to his hotel room. He threw the Doctor's files on the desk along with his change when he got inside.

"I must be crazy to think that a blue British police box is just going to just land in San Francisco. At least I can enjoy the spring here for a bit longer. I took a week for this trip," Fox mumbled to himself.

He heard his cell phone ring again, and of course it was A.D. Walter Skinner.

"I swear, I wish he'd back off."

Tossing it on the bed, he started to make his way to take a shower.

He heated up the leftover pizza from the fridge and a bottle of sweet tea, sitting at the desk, and read over his notes once again. It was very difficult to profile someone like the Doctor because he was very elusive.

You could never really tell where he was going to be and it seemed as though he had some kind of way to change his appearance. Either that or the title was just something that was shared between these different photographs.

It really did not make a lot of sense but he didn't give up on learning as much as he possibly could. He had to find out of the Doctor could provide any insight as to how his sister got abducted.

If he was changing his appearance, how could he change his face?

How was any of what he read possible?

He met up with a man while he was in England awhile back and purchased a lot of conspiracy type files from him concerning the Doctor. He wasn't, obviously, the only one who had noticed the Doctor's movements. He got the lead to this guy named Clive from the Lone Gunmen.

Luckily, the man had pictures that were associated with the Doctor. Files on where he'd been. He wasn't known to the general public, not that anyone was looking for him, but there was one consistent occurrence associated with the man, alien, known as The Doctor.

Whenever he was around, it was normally a sign that some kind of catastrophe was about to transpire. That was the conclusion the young man had reached and made the most logical sense. He did warn Mulder not to go looking him out because if he did, only God could help him.

Rubbing his eyes, he was growing tired fast. He had just arrived here yesterday and had not slept much.

"Tomorrow's a brand new day."

He sighed as he laid down on the bed, drifting off into a content slumber.

 **####**

 **The next morning, Washington, D.C.**

 **1997**

 **8:03 a.m.**

Scully sat outside the Assistant Director's office wondering why she had been summoned for a private meeting with Skinner at God forsaken hour. She was in the lower office working on some paperwork when she got his message.

"Scully, You can come in now," the Assistant Director said as he peeked outside his office.

She cracked a small smile as she entered his office, "Good morning, Sir."

"Good morning, Agent Scully. I asked you up here because I would like to know if you've heard anything from Agent Mulder. It seems as though he's made an unauthorized trip to San Francisco and I've been trying to contact him. I did speak with him briefly but, apparently, we lost connection last night. He stated in the report it was to track down a lead he'd gotten on an investigation. However, it doesn't state _what_ that investigation would be pertaining to."

"I haven't heard anything from Agent Mulder since last week, Sir. I wasn't aware of this trip or investigation."

"Agent Scully. I have been fortunate enough to be able to trace his itinerary and I do know his location. He is staying in a hotel just on the city limits and has rented a Buick Century. Now, he has completely disregarded nearly all the phone calls I have tried to make to him. As he is your partner, I would inform you that if he does not make an effort to contact me back with details on his trip, that the consequences that he faces will be severe. Up to and including suspension without pay. Now, I ask again: What do you know of this trip? You realize the penalty for withholding pertinent information will lead to the same consequences he faces."

"Sir, I entirely understand. I do know of one thing. I know that he is investigating some British Police Box but I'm not entirely sure of the details. I told him that the entire thing sounded completely absurd. Apparently, it some sort of spaceship."

"Christ, Scully. Is Agent Mulder on another alien hunt?"

"I'm afraid that's what it looks like, Sir."

"And, obviously, he believes this has something to do with his sister."

"It would appear to be so, Sir."

Skinner took the wire frames off his face and rubbed his temples. _How can Mulder continue to go on these wild goose chases of his_ , he wondered. Every time he does it, he only causes himself more pain than is necessary. He would think that since he knows their disciplinary arrangements, he would calm these excursions down.

"Thank you for the information and your cooperation, Agent Scully. If I do not hear back from him soon, I will be making a special trip to the west. You are dismissed."

#####

 **San Francisco**

 **1997**

 **3:00 p.m.**

The whooshing sound of the Tardis signaled its materialization in the late 20th century San Francisco park. The Doctor stood up straight and walked over to grab his tan trench coat from where he threw it hours before.

He stepped out of the Police Box and turned to lock it up. He sauntered along the sidewalk of the park as he set out to enjoy a nice, long stroll around the city to breathe in the welcoming springtime air. He didn't notice a man in a Buick parked, eyes bugged out, watching him leave.

"Oh, my. You've got be kidding me," Mulder whispered as he watched the tall, spiky brown haired man walk from the Police Box.

"It can't be."

Mulder's thoughts were once again distracted as his cell phone rang. With a look of annoyance, he picked up the phone and clicked it on, then turned it back off, hanging up on Skinner.

"Yeah, Skinner. I know our arrangements, but any punishment you give me will be worth this."

He said as he got out of the vehicle, locked it up, and sat on following the lanky Doctor.

"That's it, Mulder. You've pushed me too far," Skinner said as he slammed down his phone. He pushed the button to his secretary.

"Yes. Get me a ticket to San Francisco ASAP. I want to be there as soon as I can. I have urgent business to attend to."

"Yes, Sir," she said as she quickly began to make the arrangements.

"Mulder, your ass is mine," Skinner muttered as he got up and started on his way home to pack his things.

 **#####**

Mulder walked as stealthy as he possibly could while following the Doctor. Mulder took a few photos of the alien as he followed him throughout the shops.

The Doctor felt something odd but disregarded it, being that he was too lost in his thoughts to really care much of it.

All he wanted was to take a bit of a holiday at a time when Gallifrey was still in existence and things seemed simpler. Sure, there were always problems happening and he swore to himself that he would not meddle with anything in the time line.

He walked into a produce shop and looked over what they had for sale. Mulder walked in behind him and pretended to be interested in the goods as well, listening to the man carefully. The shop keeper smiled at the Doctor, "Anything I can help you with?"

"Just browsing a bit, thank you," he said with a kind smile. He looked at the pears and made a face at them.

"Those are the best in the state. Would you like some?"

"Oh, no. No, thank you. Don't really like pears. Always room for a banana, though," he said with a grin, picking one up. "How much?"

"That'll be a quarter, please."

Mulder watched as the tall man reached in his pocket, pulling out a coin. "Oh, dear. I'm sorry, I've only got British money. Never mind," he sighed and put the banana back. The lady looked at him leaving and picked up the fruit, rushing towards the Doctor.

"Don't worry, son. It's on the house. Enjoy," she said as she put it in his hand.

"Are you sure?"

"You could stand for a bit of food, dear. Have a good evening."

The Doctor nodded his thanks and left the store. Mulder stepped over to the lady and put a quarter in her hand before rushing out to the streets.

He watched as the lanky man ate his banana, staring into the sky at the sunset. He was an alien, something he'd been searching for years to find, but something else drew him to this creature. The way he carried himself as if he had the weight of the world on his shoulders.

 **#####**

They finally made their way back to the park. Mulder walked softly to his car and slipped back into the driver's seat of his vehicle. He watched as the Doctor entered his Blue Police Box and decided to stay there until he had a plan.

Up until this point, he merely wanted to find the Doctor. He was going to confront him the first moment he saw him but plans do change and so did Mulder's.

He noted the time was close to 10:00 at night now and let the seat lean back to make himself a bit more comfortable. He tried to keep his eyes wide open as he waited for the Doctor to reappear. Or at least he tried to keep himself awake. At some point during the night, he fell fast asleep.

He had just a moment to glance at the car's clock reading 6:30 in the next morning when he felt a hand balling the collar of his T-Shirt rather tightly.

"Agent Mulder, it seems as though you are in perfect working order. Care to explain to me why you haven't been answering my phone calls?" The A.D. said.

"Sir...Sir? How...When...What..."

"Good morning to you, too, Sunshine. The hotel owner told me you'd be at this park. I took the first plane out of D.C. yesterday and got here as quickly as I could. Now that I have answered your questions, would you care to explain to me just what in the hell is going on with you?"

"Sir, I can explain. My investigations are correct and I've found-I have found the Doctor."

"Who the hell is the Doctor? We have doctors in D.C."

"Sir, not a doctor. _The_ Doctor. Look, I've been sitting around this park for the last few days. The police box was not, I repeat, not here in all that time. In fact, there are no British Police Boxes in San Francisco, why would there be? That one just popped up out of thin air and this tall, brown haired creature just walked right out of it. Tell me that doesn't seem odd to you, Sir?" Mulder explained as he pointed at the British Police Box across the park from them.

Skinner let go of Mulder's shirt and opened the car door, pulling the younger man out of the car and pushing him against the Buick roughly.

"The only thing that I find odd is that the last few months you and I have formed a relationship that is completely out of protocol. You agreed to be taken under my hand and to be disciplined when you go too far. Remember? When you let that criminal out and put that little girl in danger? Now, you have repeatedly ignored my phone calls, made unnecessary requests for financing this little trip of yours, and you hung up on me, Fox Mulder. You deliberately hung up on me. Now I ask you again: What in the hell is wrong with you to be in complete insubordination of my authority over you?"

The tall Gallifreyan was standing no more than ten feet away from the two men. He had been listening to the entire conversation quietly. Mulder locked eyes with the Doctor and Skinner's eyes were holding Mulder's gaze.

Slowly, Skinner looked over his shoulder.

The Doctor's stare was stone cold as he looked upon them.

He stood with his hands in his pockets, head held high, and utterly expressionless, "Hello, I'm the Doctor. Top of the morning to both of you and all that. By the way, would either of you care to explain why _that_ one has been following me about and why he slept out here all bloody night?"

 _ **TBC**_


	2. Chapter 2

**Chapter Two: Compassion for the Stranger**

 ** _Summary: The Doctor vents some repressed emotions and Skinner proposes a unique way of helping him. Will the Doctor accept?_**

 ** _Warnings: No spanking in this one...yet._**

 ** _Disclaimer: I don't own either the DW characters nor the X-Files Characters that this fan fiction is based. I'm just having a bit of fun writing this._**

* * *

The Doctor nodded towards Fox, expecting an answer.

Skinner released his hold gradually off of Mulder and turned to face the alien. Mulder put his hands on the car behind him to steady himself as he looked in awe at the Doctor. They couldn't tear their eyes away from the alien and all that could be heard was the echo of each of them gulping.

Skinner turned around slowly and looked the tall, lanky man up and down. Mulder walked closer to the Doctor to introduce himself, "My name is Fox Mulder. I was just. Um. I-"

Mulder cleared his throat and tried to shake the sleep from his mind as well as being confronted by this alien. He never, for one moment, expected that this creature would make the first move.

"You were just…what?" the Doctor smirked at the other man's discomfort. Amused.

"I fell asleep in my car last night and then he-"

"I'm Walter Skinner. I woke him up. Thanks for the introduction, Mulder. Now, who are you?"

"See, the way this works is, my question gets answered first. No cheating. It's not proper. In any case, I've already answered that. I'm the Doctor," he said as he moved closer to Fox. "Now, why have you been following me? What is it you want?"

"What makes you think I've been following you?"

"Well, many things. You paid for my banana yesterday for one. You've been taking photographs of me. And, I came out here last night and put that blanket over you. Didn't want to wake you. You did look rather comfortable."

Mulder looked in his car and saw a blue blanket in the front seat.

"I. How did-"

"Time Lord. I can feel things more than most. Now, what is it that you want?"

"Time Lord?" Walter stared at the two men.

"I've been following you because I've gathered information that you may be an alien from another planet."

"Yes. Well, Time Lords aren't from this world."

"So, you are an alien."

"Yep. So, if that's all you wanted to know, I'll be on my way then. You two look as though you're in the middle of something anyways, " The Doctor said as he clapped his hands and walked towards his Police Box. "Really, quite lovely to have met you both but I do need to push along now. I hope that gets sorted out and best of luck with that."

The Doctor walked quickly back to his Tardis. He knew he should have left long ago but his curiosity got the better of him yet again.

When he got back to his Tardis and put his hand on the door, Mulder put his hand on the Doctor's, "Doctor, I know exactly who you are and I'm not letting you go that easily. I've been waiting here for you and am not about to let you slip through my fingers."

"You asked your question and I answered it. Now, all I want is to go and I'll be out of your hair. Yeah?"

"I've only just woken up. I have no intention of letting you leave. Even if that means arresting you."

"Arrest me for what?"

"Failure to comply."

The Doctor bowed his head and closed his eyes for a moment. He knew that he had been trapped and he wasn't exactly sure who this Mulder was and what kind of name is _Fox_?

"Fox, it would serve you well to remove your hand from mine. I will be leaving now. I don't know what you have in mind for me. Whatever it is, you can erase that idea right now. I've had a rotten week and you will only compound the problem."

Mulder took the Doctor's arm, putting it behind his back with a bit of pressure, and kept the thinner man against his Police box standing directly behind him.

"No, you don't understand. I am an FBI Agent and if I have to, I will arrest you. I have all your history, all your files with me, and I know that every time you are around trouble follows. You will answer my questions or we will do this the hard way."

The Doctor grimaced as his face was pushed against the blue wood of his Tardis. He gritted his teeth as he was on the verge of losing his temper and didn't care what the consequences would be if this human didn't back off of him right now.

"I've already answered your bloody questions, Fox. I'm an alien. I am not here to cause problems. Now, kindly let me go or -"

Skinner rushed towards both men and proceeded to break them up, "Mulder, let him go right now and tell me what's going on here."

"This man, the Doctor, is an extraterrestrial. I have been investigating his files for the past few years and every time he surfaces, he brings with him trouble. I intend to question him and find out exactly what he wants and why so many people disappear when he's around. I want to know if he is abducting people."

All the while keeping his hold on the Doctor.

Skinner looked at them both, not sure what to make out what he was hearing.

"Please, just let me go. I will leave and we can forget this entire thing ever happened. I just want to be left in peace, don't you understand?"

"What's inside the Police Box?" Skinner spoke up.

"Nothing really, just where I live," The Doctor said.

"It's his spaceship," Mulder stated.

"Spaceship? Mulder, how do you know that's a spaceship?" Skinner asked.

"I've already explained that to you, Skinner. It just appeared out of nowhere and I know because I've had this area under surveillance while I've been here this week."

"You say it is a spaceship, he says it's not. Doctor, let's take a look in there and see exactly what's on the other side."

The Doctor took in a deep breath and felt his hearts pounding. Here he was, being held by two FBI agents, and they were wanting to see inside his pride and joy. He could probably take on the one holding him if he really wanted but the other man was far too large.

He was nonviolent in either case and that thought fled his mind as quickly as it had entered it.

He shut his eyes for a moment and tried to regain control of his emotions. He nodded and answered them, "As you wish."

Mulder released his grasp on the Doctor and he immediately straightened out his coat. He ran his fingers through his hair and took the key out of his pocket with a trembling hand to the Tardis.

Mulder and Skinner walked behind him in toe inside the Tardis. They looked around the Tardis in amazement.

"It's bigger on the inside."

They both said in unison as the Doctor mouthed their words and took off his trench coat, throwing it to the side and letting it hang off the inside.

"Right, yes it is. Now, you've seen the inside. A _very_ large spaceship on the inside and lots of buttons, bells, and whistles. I'd give you a complete tour, but really, I need to be moving along now."

Skinner shook his head, "I never thought ...I can't believe...this is a spaceship?"

"Well, actually it's called a TARDIS. Time and Relative Dimension in Space."

"What's all that mean?" Mulder asked.

"It's just a fancy little name for the old girl. She can travel to any time or place in history, the future, and all that timey wimey stuff." The Doctor told them and jumped at the sudden spark through his right hand. "Oh, alright. You're not that old."

Mulder noticed and tilted his head, "What was that about?"

"Ah, she's just a bit sensitive about her age," The Doctor answered with a smirk, shaking his hand to relieve the pain from the sudden jolt.

Skinner walked around and inspected everything. In all the time he has known Mulder and his foolish ideas of aliens and spaceships, here he was in one with him.

"See, Skinner? I told you that I was right. All these years, you finally have to admit it that the X-Files aren't just some ghost stories and they actually hold merit."

"Mulder, I am perfectly aware of what I see. I know where we are. It still doesn't negate the fact that you are in a world of trouble over your insubordination."

"But, Sir. I am right. Doesn't that count for something?"

The Doctor listened to the pair and chimed in, "I see that you two really do have some matters to deal with. Now that you've seen that I do exist and, I don't mean to sound like a rude host here, _but_ would you both mind if I just move along in my travels?"

"You aren't going anywhere. If this part is true, then the other parts of my investigations are true. You've been abducting people? Where are they? They belong with their families."

"Mulder, listen. I don't have anyone on board my Tardis. I am completely and entirely alone. I don't abduct people and the ones in whatever files you got on me were my companions that traveled with me by their own free will. They aren't with me any longer."

"How can I believe you? Surely you got someone around here. Maybe doing some experiments on them?"

"There. Is. No. One. Here."

Mulder was tired of all the years he had looked for his sister with no answers and now an alien was right in front of him.

"I don't believe you."

Skinner pushed in, "Mulder..."

"No, Sir. Let me handle this. I will find Samantha and he is the only link I have that is consistent with abductions and alien activity," said Mulder as he started to move down one of the halls of the spaceship. "Samantha Mulder. Where is she? Is she kept in some sort of laboratory in here? I'll just have a look."

"You will back off now and stop. You have zero proof the Doctor took Samantha."

Mulder swung around and pointed at the Doctor, "He's an alien isn't he? He's not even a human, he's not from this planet, and every piece of data on his file only shows destruction and chaos."

"Mulder. Fox. Whatever your bloody name is - _I did not take your sister_. I have never had a companion by the name _Mulder_. You wanted to know who I am? I am a Time Lord. I can go anywhere in time and space that I want. I have taken companions before. I _never_ abducted them, they went on their own free will and they always had a choice to go or to stay. Me? I have no choice, I can't just go back to my home planet. My planet is destroyed, it's gone. I am the last of my kind. Right now, I have no companion, I have nobody because I _**am**_ too bloody dangerous. You have no idea what I've been through, what I've put others through! It'd be best if you just get off my ship right now and forget you ever saw me. Both of you."

Mulder and Skinner didn't know how to respond to what the Doctor just said. They just watched him as he walked over to the console and put his hands on the board, lowering his head, and visibly trembled before them.

"I had to destroy my own planet in the great Time War. My people, everything, it all got so terrible. I had to do it. I didn't want to do it. I was the only one who could stop it! Then, I came back here and found Rose but then I lost her. She's in another reality. I had to break my other companion's heart because she got entirely too close. I had to wipe Donna's memory completely or the mere thought of _**me**_ would cause her mind to completely melt down. Quite literally."

The Doctor took in a deep breath and turned to face Mulder. Staring him directly in the eye, he moved to him as he spoke dangerously low. "You're right, I'm not human. I am the very last of my kind and I am so very alone. So, please. Forget me. Don't try to dissect me or figure me out. I am just one species of so many different types of creatures out there."

Skinner felt an ache in his heart for this creature. Mulder didn't know what to say, he felt so horrible for what he had implied about the Doctor. Skinner walked behind the Doctor and put a hand on his back and whispered, "I don't know you but I am sorry, Doctor."

The Doctor turned around nodded, trying to calm the shaking in his hands.

"I'll be fine. Always am. But I would rather you both just leave. Please. I don't mean you or anyone on this planet any harm."

Skinner whispered gently, "I know you're in a lot of pain right now, Doctor."

"That really doesn't matter right now. I am here on holiday which has now been cut short. I'll be on my way."

The Doctor pointed towards the door and hoped they would take the hint. He shouldn't have let them in. He shouldn't have given the younger man a blanket. He had to stop caring so bloody much.

Skinner may be a strict disciplinarian, but he also had a soft heart and he truly hated seeing another being in so much anguish.

Mulder walked over to the other two and swallowed hard, "I'm so sorry, Doctor."

The Doctor looked up at Mulder for a moment, "I've done a lot of things, but I swear to you, I never took your sister, ever. There is nothing for either of you to be sorry about. Can you both please just do as I ask and leave now?"

Skinner patted the Doctor on the back and sighed. He helped the man to sit down and said, "I'll be right back, Doctor. I just need to tell Mulder something and I'll return, okay?"

The Doctor looked up at him and nodded, "Fine."

Skinner walked slowly over to Mulder, rubbing his head, and led the other man outside. He bowed his head and looked over the top of his glasses at Fox.

"Mulder, I don't know what you've gotten yourself, ourselves, into with this. Now, you've ran free the last few days and you will listen and obey my orders to the letter. Understand?"

"Yes, Sir."

"You will be punished for what you've done. You know what you did and there is no need to explain. You go back to your Buick and drive to the hotel. You will wait for me there until I arrive and I will deal with you. Right now, this man, this alien, he needs someone. I am going to stay with him and try to do what I can for him. I can't leave someone when they need help. Do I make myself clear, Agent Mulder?"

"Yes, Sir."

The Doctor moved from the door, listening in on the conversation between the two. He squinted his eyes, wondering what Skinner meant about punishing Mulder.

Mulder knew it was best not to argue with his superior. He had made so many mistakes the last week that he figured it would be the wise move to make. He went over to the Doctor and gave him a sympathetic look, "I am sorry about the way I talked to you."

And then, Mulder left to follow Skinner's instructions.

He shook his head as Skinner walked back into the Tardis and excused himself to the bathroom. He looked at himself in the mirror and whispered, "Well, don't I look just brilliant?"

After splashing a bit of water on his face, he turned around and got a fresh towel. He ran a comb through his hair, making it stick up in just the right places, and finished freshening up. He walked back out to the main room of the Tardis and saw Skinner was still here.

"Hello. Would have imagined you'd of left by now."

"Thought I'd stick around for a little while to see how you were."

"Me? Ahhh. Well, I'm going to be just fine. I'm always fine. Your friend just kind of got the better of me there and I unleashed a lot of pent up things inside. Sorry about that really. I'll be right as rain though. You can go on if you want and I'll just move on out of your hair."

The Doctor looked at Skinner with a cheeky grin, "Or lack thereof."

Skinner cocked an eyebrow and folded his arms over his chest, "Now watch it there, young man. I stayed around to help you, whether you want it or not."

"Well isn't that something? Me? Young man? Hah!"

"You do look a bit younger than me and you don't have a shred of grey hair."

"I assure you-Skinner was it? I am quite old indeed. I'm about 900, give or take a few years."

"You're really 900? That's a long time."

"Tell me about it. Seen a lot of things."

"Well, I don't know much about aliens or Time Lords. But, you do look like you have most of the same make up as us humans do. And you have emotions," Skinner said as he walked closer to the Doctor. "I am going to offer to help you through those emotions, Doctor. If you have lived this long, you don't want to carry on the rest of your years with so much guilt."

"And how, my new friend, do you propose to do that?" He picked up his sonic screwdriver and moved towards the console.

"There are many ways we can work through it. Some through talking."

"Oh, I love to talk."

"So, what's really on your mind?"

The Doctor looked up at Skinner who was about to touch a knob, "Don't touch that."

"What? That? Why not?"

"Because I don't feel like fixing it later."

"Hmm."

"Anyways. What other ways do you humans work through your emotions?"

"Some through talking. Some through an ancient method. I use it on Mulder actually."

"Really? He likes ancient methods, does he?"

Skinner rubbed the back of his head and cleared his throat, "Well, I doubt he likes it very much or enjoys it. He does accept it to help work through his own guilt."

The Doctor sat on the floor with wires over his shoulders and fixed his glasses to get a closer look at them. Skinner watched the man in an amused way, finding his mannerisms fascinating.

"So, are these ancient methods how you propose to help me?" The Doctor asked, not really appearing to be paying attention to Skinner but he was in his own way. Why was this man still here anyway?

He had his back turned to him, sitting on the floor while running scans with his sonic screwdriver over the Tardis to make sure everything was working properly.

Skinner stood in front of the Doctor and said loudly to get the Doctor's attention, "I intend on helping you the same way I help him, yes. A bit of punishment, if you will, so you can feel atonement for the sins you feel you've committed and forgiveness once it's all over."

The Doctor felt his hearts stop and dropped some wires into his lap at that word: _punishment_. Did this human really just say what he thought he said? He looked up at Skinner and whispered, "What?"

"Look at me."

Slowly the Doctor met Skinner's eyes. Suddenly, the Doctor felt incredibly small as the Assistant Director towered over him. "What sort of punishment are you talking about, Skinner?"

"Have you ever heard of spanking or corporal punishment?"

The Doctor swallowed and nodded, "I've run across that term before. How in the bloody hell is that going to help me? You use that on Fox? That's a rather archaic method. And well, corporal punishment is being phased out. Almost completely."

Skinner had taken Mulder under his wing not too long ago and the first mention of this got a similar response from his subordinate. He had always been the dominate type and he could always tell when someone needed help. He didn't know this Doctor but he could tell when someone needed a strong hand to guide them.

"Almost isn't completely, though. Have you ever been punished, Doctor?"

"Well-" The Doctor said as he took off his glasses.

"Not a spanking or anything. We didn't have those kinds of punishments on Gallifrey. When one of us did something requiring punishment at the Academy, it was handled differently. I've never been, or had to be, spanked as you call it. I imagine that it is rather painful though."

"It certainly can be, Doctor. It has been used on our planet for centuries and is a good form of catharsis. Something I can tell you need right now. With everything you told me when you were talking earlier, I can tell one is required."

"Well, I don't know, Skinner. I feel fine right now. I know I said a lot of things and, really, I thank you for listening to me and all that. I doubt a spanking will serve much good for someone like me. I just needed to get a lot of things off my chest. Thank you for the offer," the Doctor said and pushed the button on his screwdriver to its appropriate setting, attempting to get back to work.

"I figured you would say something like that, Doctor. Receiving a spanking is not an easy thing to submit to. But you are going to get what is coming to you: whether you want it or not. Now, put that thing down and stand up."

The Doctor cleared his throat and looked up at Skinner. He turned his sonic screwdriver off and put it in the inside of his coat pocket. He moved to his feet and stood in front of Skinner, "I will have to disagree with you, Walter. No spanking the Doctor today. Shouldn't that sort of thing be done by my consent in any case?"

"You do have a point there, Doctor. However, I do believe it's in your best interest to consent."

"Oh, now Walter! You scarcely know me and we've not even had a first date."

"Now, don't you get smart with me."

"See, that's rather hard not to do. I am, well - quite frankly, brilliant," the Doctor grinned and shoved his hands in his pockets, rocking back and forth.

"From here on out, Doctor. You will refer to me as 'Sir'. If you don't, your punishment will be that much worse on you," Skinner informed him as moved his fingers to his belt.

The Doctor ran his fingers through his hair and contained a the chill from running up his spine at that word. He started moving quickly around the Tardis, "Alright, Sir," he started and snapped his fingers. Skinner keeping his eyes on the Doctor and not noticing the doors of the Tardis opening up.

"I understand your point of view and I can respect that. However, from a Time Lord's perspective, your train of thought is rather flawed in about three ways. For one, I barely know you, a stranger, and letting you spank my bum is rather odd. With that said, the second point that I would like to make is that I would rather get to know you first before I go over your knee. A rather muscled looking knee, I must say." The Doctor grinned and moved closer to Skinner.

"And the third?" Skinner tilted his head.

"Well, I would like to know what you plan on spanking me with. A belt? A paddle? A cane?"

"You want to see my implements?"

"Well, I have to make an informed decision and I would need to take everything into consideration before, as you call it, consent. How well we get on, what you plan on using, and other such things."

"I do have my bag in my car outside. I suppose I could go get it and show you what I would be using."

"Brilliant! Please, do go get it."

Skinner turned around and nodded, arching a brow. "No tricks?"

"Nope. None at all," the Doctor said with a grin.

"You'll be here when I return?"

"Yep."

Skinner walked outside the door to his vehicle to retrieve his bag full of spanking implements. As soon as he left, the Doctor raised his hand up in the air and snapped his fingers again - closing the doors.

"By the way, Walter Skinner, Sir. Rule number one: The Doctor lies," he said with a blank expression to the doors. He rushed to his console and flipped a few switches, pulling down a lever.

As the Tardis vanished from Skinner's sight, he dropped his bag to the ground and could only hear a very faint voice over the wheezing sound of the Tardis.

"Allons-y!"

 _ **-TBC-**_


End file.
